Editor bug when annotating pdf and copying refs

I was using the including pdf features in the app, highlighting, copying refs, pasting them into a page. However, at some point, I was just writing notes in the same page all all of a sudden the app started freaking out. I believe it duplicated the window, but I’m not sure how.

Afterwards, all the copied refs became unlinked in the pdf. They no longer link back to their place in the pdf and the sections they were linked to are no longer highlighted.

I am not sure what caused this and I do not have much other than my description of the event, but please let me know if there is any other information I can provide.